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Verified Commit 59c1681f authored by Laurent Modolo's avatar Laurent Modolo
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ucsc: rm non working BigWigToWig convertion (see bioconvert)

parent 759a77c9
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......@@ -30,57 +30,3 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \
${bg.simpleName}_norm.bw
"""
}
params.bigwig_to_wig = ""
params.bigwig_to_wig_out = ""
process bigwig_to_wig {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.bigwig_to_wig_out != "") {
publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
}
input:
tuple val(file_id) path(bw)
output:
tuple val(file_id), path("*.wig"), emit: wig
script:
"""
bigWigToWig ${params.bigwig_to_wig} \
${bw} \
${bg.simpleName}.raw
awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.raw > ${bw.simpleName}.wig
"""
}
params.bigwig2_to_wig2 = ""
params.bigwig2_to_wig2_out = ""
process bigwig2_to_wig2 {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.bigwig_to_wig_out != "") {
publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bw_a), path(bw_b)
output:
tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig
script:
"""
bigWigToWig ${params.bigwig_to_wig} \
${bw_a} \
${bw_a.simpleName}.raw
awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.raw > ${bw_a.simpleName}.wig
bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_b} \
${bw_b.simpleName}.raw
awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.raw > ${bw_b.simpleName}.wig
"""
}
\ No newline at end of file
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